iBooks: It was understandably my first option. Now it may seem limited when compared to Marvin, but it is not a bad reading app, and one has to concede that offering a lot of choices like Marvin is not Apple's way of doing things. The one feature that got me hooked on iBooks, instead of the once revered Stanza, was the ability of synchronizing reading positions, highlights and annotations. Nowadays I have an iPod Touch (5th generation) for ultra-portable reading (sorry, I don't think the iPad Mini would fit into my pocket) and a full-sized retina iPad (3th generation) for cozy reading at home. Being able to change devices easily is a must. I've heard of people who perform this syncing by hand. Honestly, I'd have to fall in love for an app to tolerate such a hassle (although I can understand people who chose to do it after falling in love for Marvin). For this same reason I've been turning down other apps that are highly rated around here (Bluefire and ShuBook come to mind). My iBooks library has increased considerably, and I don't have many reasons for complaint.
Kindle: As an Amazon customer, Kindle is a no-brainer. It is also a quite decent reading app. I like the Caecilia font a lot; the app runs smoothly; the Whispersync works like a charm; and I really, really appreciate the way dictionaries are handled (and it got even better after the iOS apps started accepting third-party dictionaries, what is very useful to language learners). And Amazon provides 5Gb of cloud storage for personal documents.
Readmill: I find it puzzling the little love Readmill has been getting around here. My first impression when trying it was: "such a beautiful display of text!" Since my days of e-reading on a Palm device (whose 320x480 resolution on a 3.7'' screen —therefore slightly inferior to the non-retina iPhone— was deemed high), when apps just showed text, with as few visual options as selecting font size, I feel glad that nowadays reading apps have been taking seriously the aesthetics of text display. Readmill excels at that point. Besides, it offers cloud storage for ebooks and all those bells and whistles of "social reading", which is rather interesting.
Marvin: What can I add to all the praising? Marvin surely puts iBooks to shame! Marvin is a joy to discover, in all its features. I have set up the configurable buttons to access some online bilingual dictionaries and translation services. This makes Marvin, besides Kindle, the best options for reading in a language being learned. Nevertheless, so far, I've been using Marvin far less than its alternatives, mostly because of the (temporary) lack of an iPhone version. You can bet I've been
waiting anxiously for it! With Marvin 2.0, I'll certainly be transferring some ebooks from iBooks, Kindle and Readmill.
Kobo: I'm also a Kobo costumer, through its Brazilian partner, Livraria Cultura. It is ok, but nothing to write home about. I'll certainly not be sideloading ebooks on this thing. I've experienced some errors in the syncing of highlights, notes and reading positions. At least, I know Readmill is compatible with Adobe DRM, and this way I'm not stuck with Kobo.
GoodReader: My option for PDF ebooks. I see people in this forums have other choices, but I find GoodReader hard to beat. The margin cropping alone is worth it. I read PDFs only in the iPad, because squinting at them on a small screen doesn't fit my definition of reading pleasure. So, no syncing required.